Tag: dbNSFP

Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

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Discrepancy between the downloaded clinvar, dbNSFP and website

Discrepancy between the downloaded clinvar, dbNSFP and website 0 Hi All, I encountered discrepancies in clinvar annotations, leading to inconsistencies: Discrepancies between locally downloaded datasets from clinvar and dbNSFP_CLINSIG and their respective web versions were noted. For instance, the variant (chr2:21006288:C:A) was labeled as Pathogenic in the downloaded datasets but…

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VEP ensemble docker and plugins

VEP ensemble docker and plugins 0 Hi, I have used VEP in local using docker and cache and ran this command sudo docker run \ -v /mnt/dodl_drive/sarek_cc/vep:/data ensemblorg/ensembl-vep \ vep -i input_sample.vcf \ –cache \ –output_file output_sample.vcf \ –everything which ran successfully and the output VCF also is as expected….

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Whole exome sequencing and transcriptome analysis in two unrelated patients with novel SET mutations

Moeschler JB, Shevell M, Committee on G. Comprehensive evaluation of the child with intellectual disability or global developmental delays. Pediatrics. 2014;134:e903–18. PubMed  Google Scholar  Patel DR, Cabral MD, Ho A, Merrick J. A clinical primer on intellectual disability. Transl Pediatr. 2020;9:S23–35. PubMed  PubMed Central  Google Scholar  Baker K, Devine RT,…

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Finding Unique values on specific INFO field of the VCF file (dbNSFP, vep annotated multisample VCF)

Hello everyone! I searched the forum but coundn`t find a question that is like mine I have a multisample annotated VCF file (with dbNSFP plugin) to which I have filtered using VEP, like so: /scratch/ensembl-vep-109/ensembl-vep/filter_vep –force_overwrite –input_file {1} –output_file /home/filtering/2/2_{1/.}.vcf –only_matched –filter “(clinvar_clnsig is Pathogenic) or (clinvar_clnsig is Likely_pathogenic) After…

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Not all variants are annotated with AF

Forum:Not all variants are annotated with AF – expected or a problem? 0 I tried to use built-in databases and build my own (snpEff), however, in both cases, not all my variants are annotated with Allele Frequency (AF). The problem is: those variants not annotated in VCF has Alelle Frequency…

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Issue with dbNSFP using SnpSift

Issue with dbNSFP using SnpSift 1 Hi everyone, I’m having trouble annotating a VCF with SnpSift and the dbnsfp option. From the documentation, running: java -jar SnpSift.jar dbnsfp -v -db path/to/db path/to/vcf > out.vcf …should annotate for all fields in the database. However, it seems that my files are only…

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Genome-wide prediction of disease variant effects with a deep protein language model

This study did not require any ethical approval. ESM1b In this study, we have leveraged and expanded the use of ESM1b, a protein language model developed by MetaAI20. The code and pretrained parameters for ESM1b (and other ESM models) were taken from the model’s official GitHub repository at github.com/facebookresearch/esm. Throughout…

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snpEff and SIFT calculation

snpEff and SIFT calculation 0 Hi, I annotated my VCF files using snpEff by creating new database (I use own assembly and gtf file). I would like also to calculate SIFT (prediction of consequence in missense variant). I found, that I can do this using snpSift, but I see that…

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error related to SnpSift

error related to SnpSift 1 hello everyone, I am trying to use annotate function of snpsift. I have downloaded the software using conda. when i write the command SnpSift this is the output: SnpSift version 4.3t (build 2017-11-24 10:18), by Pablo Cingolani Usage: java -jar SnpSift.jar [command] params… Command is…

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Deep exome sequencing identifies enrichment of deleterious mosaic variants in neurodevelopmental disorder genes and mitochondrial tRNA regions in bipolar disorder

GBD 2016 Disease Injury Incidence Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet. 2017;390:1211–59. Article  Google Scholar  Kato T. Current understanding of bipolar disorder:…

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dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations | BMC Genomics

MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The database of genomic variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42(Database issue):D986–992. Article  CAS  PubMed  Google Scholar  Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the…

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Annotating with CADD, gnomad, Clinvar & dbNSFP on UKB RAP – Feature Requests

dint May 9, 2022, 1:33pm #1 i’m just wondering if you can specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab_spark_cluster o the UKB RAP? From the hail website, the following command can be used on your matrix file to annotate with these features: db =…

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wrong number of fields ?

Error occurence after merging files with bcftools: wrong number of fields ? 1 I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff, SnpSift. first pair vcf -> only variations| CASES and CONTROLS second pair vcf -> variations + SnpEff | CASES and CONTROLS third pair vcf->…

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Failed to instantiate plugin dbNSFP in VEP

Failed to instantiate plugin dbNSFP in VEP 0 Hi Team, My VEP (version 105, installed by perl INSTALL.pl) works well. But I face some problems to use dbNSFP plugin (also installed by perl INSTALL.pl) with VEP tool. My dbNSFP version 4.2a was installed by the following code without any warning…

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Missense Variant on hg19

Missense Variant on hg19 1 Hello everybody, I am using plink for doing some statistic studies on a SNP set. I would like to use only missense variant, and I have the IDs of my SNPs of interesting. Can someone suggest me how can I download a database of homo…

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VEP plugin uses

VEP plugin uses 0 It is a small question, I downloaded all plugins and wrote in the input script to get plugin experimental functionalities (I am using merged cache Ref_Seq & Ensembl both). # make a file with a single variant using bash echo “17 43071077 43071077 T/C + variant_1″…

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Interpreting dbNSFP prediction scores

Interpreting dbNSFP prediction scores 1 How should I interpret for example, SIFT score: SIFT_pred = T;T;T;T;D;T SIFT_score = 0.138;0.138;0.138;0.138;0.042;0.157 From dbNSFP documentation, I understand the meaning of D and T D: Deleterious (sift<=0.05); T: tolerated (sift>0.05) My question is: Why there are multiple values of both pred and score in…

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